There are growing calls for a nationwide investigation into abuse within the Catholic Church, after explosive new claims about boys dying in care, victims being silenced, and police investigations being stymied were made public.

Victims' support group Broken Rites says it has evidence that two orphaned boys died while in the care of the Hospitaller Order of St John of God in Victoria - one of them after being thrown down a flight of stairs.

Broken Rites says it will present its evidence to the ongoing Victorian parliamentary inquiry into the handling of child abuse and says it wants a nationwide royal commission to look into abuse claims.

Meanwhile, a senior New South Wales police officer says there has been a systematic cover-up of organised paedophilia by the Catholic hierarchy in his state.

In an open letter to New South Wales Premier Barry O'Farrell, Detective Chief Inspector Peter Fox alleges the church covers up for paedophile priests, silences investigations, and destroys crucial evidence to avoid prosecution.

Detective Chief Inspector Fox's call for Mr O'Farrell to set up a royal commission has been echoed by New South Wales state MPs and even the Bishop of the Maitland-Newcastle diocese.

Federal Government Minister Bill Shorten says he is not convinced a national investigation is the answer.

However the church is also under fire for running its own system for looking into sexual abuse, with a Victoria Police adviser saying that wresting control from church investigators is the "number one issue".

Alleged deaths

Broken Rites says it is preparing to tell the Victorian inquiry that two boys - orphans who had been left without any family members - died while in the care of the Hospitaller order at Lilydale and Cheltenham in the 1960s.

Spokesman Dr Wayne Chamley says survivors have passed on the stories.

"One of those was in a bed beside a man that I did a mediation for," he told ABC local radio

"That man said that that boy had just recently arrived in the orphanage, and when he woke up the child was dead."

"The other one was thrown down a set of staircases."

Dr Chamley says he worked with police for eight years to try and move the investigation along.

"The police were just never resourced. They were never resourced to get to the bottom of this," he said.

We need a Commonwealth-initiated royal commission into all this. There's too much going on all over the country. It's not in the past. It's still going on now.

Broken Rites spokesman Dr Wayne Chamley

Dr Chamley says the cases were put on the public record in 2004 when he testified before a Senate inquiry, and he is now calling for a national royal commission of inquiry.

"We need a Commonwealth-initiated royal commission into all this. There's too much going on all over the country," he said.

"It's not in the past. It's still going on now.

"The big problem now is visiting priests. They fly in ... nobody knows what their bona fides are."

The parliamentary committee has revealed it has taken steps to get documents from the Catholic Church as part of its inquiry.

The committee is hearing from people who work on sex abuse investigations for Victoria Police.

Patrick Tidmarsh, a Victoria Police adviser, says it is extraordinary that the church has its own system for dealing with allegations of child sex abuse.

"I don't think they should be investigating themselves. I think that is absolutely the number one issue," he said.

"I find it personally extraordinary that an organisation has set up a separate system, particularly one where if you volunteer for that system, you give up your rights to any other system."

Mirroring police evidence given to the Victorian inquiry, the senior Hunter Valley detective says in his letter: "Many police are frustrated by this sinister behaviour which will continue until someone stops it."

"I can testify from my own experience that the church covers up, silences victims, hinders police investigations, alerts offenders, destroys evidence and moves priests to protect the good name of the church. None of that stops at the Victorian border."

Abuse statistics for the Newcastle-Maitland diocese paint an ugly picture:

400 known victims of child sexual abuse by clergy

11 clergy charged and convicted since 1995

6 Catholic teachers convicted since 1995

3 priests currently on trial

First priest charged this year with concealing the crimes of another

12 priests involved in substantial compensation claims

Highest known compensation payout to a victim - $3 million

Two police strike forces are already investigating whether church officials were involved in covering up crimes.

I had other priests that hadn't been charged with anything removing evidence and destroying it before we were able to secure it, and we just went around in circles.

Peter Fox

Not all clergy are fully cooperating with police, but Mr O'Farrell has repeatedly said police have the investigation under control.

But Chief Inspector Fox believes police prosecutions on their own cannot deal with the Catholic Church's structures and systems for reporting abuse.

"In many cases that I came across, one priest who had previously faced paedophile charges was donating parish money to the legal support of another priest to defend himself from those charges," he told Lateline.

"I had other priests that hadn't been charged with anything removing evidence and destroying it before we were able to secure it, and we just went around in circles.

"The greatest frustration is that there is so much power and organisation behind the scenes that police don't have the powers to be able to go in and seize documents and have them [the church] disclose things to us."

Chief Inspector Fox says he has "definite information" of alleged cover-ups by a number of diocese bishops.

He says a royal commission into allegations of abuse and cover-ups is needed because police do not have the powers to mount a proper investigation.

"There's so much that the police force can't do. We don't have power," he said.

A spokesman for Mr O'Farrell says he believes the best result will be successful prosecutions and he has urged anyone with information to go to police.

But the detective's calls for a royal commission have been backed by state MPs from both sides of politics.

Troy Grant, who holds Dubbo for the Nationals, says Sydney Archbishop Cardinal George Pell has failed to address child abuse allegations and should be replaced.

"He's been in charge for a long time and he's abjectly failed the parishioners of the Catholic Church," the former policeman said.

"He's abjectly failed this nation from that institution's position. I'm on the record as saying that's where the first decisive step needs to occur."

Greens MP David Shoebridge has accused Mr O'Farrell of avoiding the issue.

"If it was any other organisation with a history of systemic repeated criminal acts there would be no question about a royal commission," he said.

"But I've got to say the church is particularly well-connected in politics in New South Wales.

The Bishop of the Maitland-Newcastle Catholic Diocese says a royal commission into child abuse by clergy would probably clear the air.

"I'd welcome it," Bishop Bill Wright said on Radio National.

"I think it'd give satisfaction to a great many victims to have everything out there on the table, and I think in many respects it would be good for us to have an independent body establish all the facts."

But he denied the church was blocking investigations into abuse by priests.

"Absolutely not," he said. "We cooperate very actively with police."

On Chief Inspector Fox's allegations he said: "I'm aware of the matter to which he's referring.

"He investigated these matters over 35 years. That is some time ago.

"My problem [with Chief Inspector Fox's] published words [is that] he writes as if he's talking about things that are happening now - the church doesn't inform police of these things, it covers up and moves people around and so on.

"At an earlier time .. people would come and tell us things and they did not wish to go to the police. We respected that.

"More recently, and largely in our own interest I've got to say, we deny their wishes ... [and] we refer all these matters to police."